My relationship fields suddenly stopped worked. When I select the posts I want to show and update, the choices are no longer saved. I tried re-creating the fields, as well. I’m running WordPress 4.0 and ACF Pro 5.0.8!
Woah, nevermind. I somehow deleted the index.php file from my theme, which I didn’t know WordPress needed to run an active theme (I thought a functions.php and other templates would suffice). Interesting to know this breaks ACF in funny ways. Anyway, fixed, but leaving this in case someone else has a similar issue!